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FIX: Properly mount local templates #2020

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merged 2 commits into from
Mar 4, 2020
Merged

FIX: Properly mount local templates #2020

merged 2 commits into from
Mar 4, 2020

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mgxd
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@mgxd mgxd commented Mar 4, 2020 •
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This PR re-enables use of custom templates after the output spaces refactoring.

The local directory where the custom template exists is now mounted to the TemplateFlow home within the container.

Related issue: https://neurostars.org/t/custom-template-fmriprep-20-0-1/6232

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effigies
effigies reviewed Mar 4, 2020
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wrapper/fmriprep_docker.py
command.extend(['-v', ':'.join((os.path.abspath(space), target, 'ro'))])
spaces.append(target)
spaces.append(tpl[4:])
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It looks like we're baking in some assumptions that the directory will be called tpl-XYZ. We should either require that (error if tpl[:4] != 'tpl-') or be a bit more forgiving (if not tpl.startswith('tpl-'): tpl = 'tpl-' + tpl).

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Sure, we can add a check to ensure the directory is compliant with templateflow standards.

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This may be obvious, but in case you're about to do a significant amount of work, I would really keep this very simple. If the error is going to show up early and be clear inside fMRIPrep proper, then we really don't need to do anything here.

I'm mostly worried about if somebody types --output-spaces /my/template and gets strange errors about "tpl-late not found", or something like that.

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since this check is happening within the niworkflows SpatialReference, that would probably be the best place for that. Since the wrapper behavior is a little different (it has to actually mount the directory), we can include a check here too

effigies
effigies approved these changes Mar 4, 2020
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LGTM.

@mgxd mgxd merged commit 86bc390 into nipreps:maint/20.0.x Mar 4, 2020
@mgxd mgxd deleted the fix/wrapper-custom-templates branch March 4, 2020 19:29
@mgxd mgxd added this to the 20.0.2 milestone Mar 4, 2020
effigies added a commit that referenced this pull request Mar 11, 2020
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Merge tag '20.0.2'
624baf3 
Merge notes:

* Fix gh-2014 appears to have been made unnecessary by gh-2018.

Tag message:

20.0.2 (March 6, 2020)
======================
A bug squashing release in the 20.0.x series.

This release fixes the use of custom templates within the docker wrapper, remedies crashes
when FreeSurfer HOME was not set, and improves the documentation for local installations.

With thanks to Blaise Frederick for the contribution.

  * DOC: Update standalone installation requirements (#2009)
  * FIX: Crashes whenever FREESURFER_HOME is not set (#2014)
  * FIX: Local template mounting (wrapper) (#2020)
  * MAINT: Pin minor series of nipype, major series of nibabel (#2021)
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